Genomic changes that influence gene expression can have significant impacts on the evolution of novel morphological traits and play important roles in diseases such as cancer. While much effort has been dedicated towards defining networks of co-regulated genes, comparatively little is known about the relative importance of processes that result in the recruitment of gene expression regulators to novel and previously unbound locations within the genome. The neo-X chromosome of Drosophila miranda represents an ideal system for studying such processes. This chromosome is young (~1 MYA) yet is already capable of recruiting a regulatory complex which up-regulates gene expression levels across the entire male X chromosome by a factor of two. This process is known as dosage compensation and occurs specifically in males to compensate for their missing X chromosome (e.g. XY versus XX). Genome assemblies from close relatives of D. miranda will be used to identify the mutational path leading to the evolution of the dosage compensation complex binding sites on the neo-X chromosome. From this analysis, it will be possible to determine the relative importance of the various mechanisms by which a binding motif evolves at a novel location in the genome, including de novo evolution from a pre-site or random sequence, transpositions from other genomic locations, or the local amplification of weak binding sites. In addition, polymorphism data from wild D. miranda lines will be analyzed to determine if these binding sites evolved under positive selection, which has implications for the process of Y chromosome degeneration. PUBLIC HEALTH RELEVANCE: This research project seeks to understand basic principles underlying the regulation of gene expression. The results of this project will be relevant to the treatment and diagnosis of human diseases caused by improper regulation of gene expression such as anemia and many types of cancer.